Brachypodium distachyon is rapidly emerged in biological study and has been currently used as a model system for genetics and functional studies for crop improvement and biofuel production. Phosphinothricin (PPT) has been widely used as a selectable agent, which raises ammonium content and induces toxicity in non-transformed plant cells. However PPT selection is not much effective on Brachypodium callus consequently reducing transformation efficiency. In order to identify the efficient conditions of PPT selection, calli obtained from mature seeds of Brachypodium (PI 254867) were cultured on the callus inducing medium (CIM) or regeneration medium (ReM) containing serial dilutions of the PPT (0, 2, 5, 10, and 15 mg/l) in dark or light condition. Callus growth and ammonium content of each treatment were measured 2 weeks after the treatment. Although callus growth and ammonium content did not show much difference in CIM, slow callus growth and increased ammonium accumulation were found in ReM. No significant difference of ammonium accumulation in response to PPT was found between dark and light conditions. In order to identify major factors affecting increased ammonium accumulation, callus was cultured on the media in combined with phytohormones (2,4-D or kinetin) and carbon sources (sucrose or maltose) containing with PPT (5 mg/l). The highest ammonium content in callus was found in the kinetin and maltose media.